{ "_id": "6ac64710f511ae58c09a95b6", "Package": "GSReg", "Version": "1.47.0", "Date": "2016-11-28", "Title": "Gene Set Regulation (GS-Reg)", "Author": "Bahman Afsari , Elana J. Fertig\n", "Maintainer": "Bahman Afsari , Elana J. Fertig\n", "Description": "A package for gene set analysis based on the variability\nof expressions as well as a method to detect Alternative\nSplicing Events . It implements DIfferential RAnk Conservation\n(DIRAC) and gene set Expression Variation Analysis (EVA)\nmethods. For detecting Differentially Spliced genes, it\nprovides an implementation of the Spliced-EVA (SEVA).", "License": "GPL-2", "biocViews": "GeneRegulation, Pathways, GeneExpression,\nGeneticVariability, GeneSetEnrichment, AlternativeSplicing", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:25 UTC", "RemoteUrl": "https://github.com/bioc/GSReg", "RemoteRef": "HEAD", "RemoteSha": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-07 10:41:06 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "GSReg_1.47.0.tar.gz", "_fileid": "https://r2.ropensci.org/b40464a80a1c667155de33ab7e32882e1d1eedc5bb38077a1b2f3cecca9c2a03", "_filesize": 592433, "_sha256": "b40464a80a1c667155de33ab7e32882e1d1eedc5bb38077a1b2f3cecca9c2a03", "_expires": "2027-01-15T13:20:14.000Z", "_created": "2026-10-07T10:41:06.000Z", "_published": "2026-10-07T13:20:16.267Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 1, "warning": 2, "note": 12 }, "_upstream": "https://github.com/bioc/GSReg", "_commit": { "id": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379965 }, "_maintainer": { "name": "Bahman Afsari", "email": "ejfertig@jhmi.edu", "login": "afsari", "description": "", "uuid": 2557586 }, "_distro": "resolute", "_jobs": [ { "job": 112751699010, "time": 231, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "11476866261" }, { "job": 112751699245, "time": 259, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11477385757" }, { "job": 112751699090, "time": 410, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11476771952" }, { "job": 112751699160, "time": 245, "config": "linux-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11476741521" }, { "job": 112751699117, "time": 369, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11477035415" }, { "job": 112751699149, "time": 184, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "11484592621" }, { "job": 112751699130, "time": 465, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11484091686" }, { "job": 112751699106, "time": 239, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11485085874" }, { "job": 112751699124, "time": 281, "config": "macos-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11483293778" }, { "job": 112749640179, "time": 340, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11476526435" }, { "job": 112751698920, "time": 204, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11476317447" }, { "job": 112751699199, "time": 300, "config": "windows-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "11476632066" }, { "job": 112751699346, "time": 413, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "11476093605" }, { "job": 112751699215, "time": 390, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "11476437733" }, { "job": 112751699419, "time": 326, "config": "windows-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "11476836637" }, { "job": 112751699200, "time": 330, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "11476422535" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.13.1", "role": "Depends" }, { "package": "Homo.sapiens", "role": "Depends" }, { "package": "org.Hs.eg.db", "role": "Depends" }, { "package": "GenomicFeatures", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Depends" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "GSBenchMark", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "generegulation", "pathways", "geneexpression", "geneticvariability", "genesetenrichment", "alternativesplicing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 473, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 528, "source": "https://www.bioconductor.org/packages/stats/bioc/GSReg" }, "_mentions": 3, "_searchresults": 19, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GSReg.html", "extra/manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "GSReg.GeneSets.DIRAC", "GSReg.GeneSets.EVA", "GSReg.kendall.tau.distance", "GSReg.kendall.tau.distance.restricted", "GSReg.kendall.tau.distance.template", "GSReg.overlapJunction", "GSReg.SEVA" ], "_datasets": [ { "name": "geneExrsGSReg", "title": "", "object": "juncExprsSimulated", "file": "juncExprsSimulated.rda", "class": [ "matrix", "array" ], "fields": [ "sample_01_N", "sample_02_N", "sample_03_N", "sample_04_N", "sample_05_N", "sample_06_N", "sample_07_N", "sample_08_N", "sample_09_N", "sample_10_N", "sample_11_N", "sample_12_N", "sample_13_N", "sample_14_N", "sample_15_N", "sample_16_N", "sample_17_N", "sample_18_N", "sample_19_N", "sample_20_N", "sample_21_N", "sample_22_N", "sample_23_N", "sample_24_N", "sample_25_N", "sample_01_T", "sample_02_T", "sample_03_T", "sample_04_T", "sample_05_T", "sample_06_T", "sample_07_T", "sample_08_T", "sample_09_T", "sample_10_T", "sample_36_T", "sample_37_T", "sample_38_T", "sample_39_T", "sample_40_T", "sample_41_T", "sample_42_T", "sample_43_T", "sample_44_T", "sample_45_T", "sample_46_T", "sample_47_T", "sample_48_T", "sample_49_T", "sample_50_T" ], "rows": 20, "table": true, "tojson": true }, { "name": "junc.RPM.Simulated", "title": "", "object": "juncExprsSimulated", "file": "juncExprsSimulated.rda", "class": [ "matrix", "array" ], "fields": [ "sample_01_N", "sample_02_N", "sample_03_N", "sample_04_N", "sample_05_N", "sample_06_N", "sample_07_N", "sample_08_N", "sample_09_N", "sample_10_N", "sample_11_N", "sample_12_N", "sample_13_N", "sample_14_N", "sample_15_N", "sample_16_N", "sample_17_N", "sample_18_N", "sample_19_N", "sample_20_N", "sample_21_N", "sample_22_N", "sample_23_N", "sample_24_N", "sample_25_N", "sample_01_T", "sample_02_T", "sample_03_T", "sample_04_T", "sample_05_T", "sample_06_T", "sample_07_T", "sample_08_T", "sample_09_T", "sample_10_T", "sample_36_T", "sample_37_T", "sample_38_T", "sample_39_T", "sample_40_T", "sample_41_T", "sample_42_T", "sample_43_T", "sample_44_T", "sample_45_T", "sample_46_T", "sample_47_T", "sample_48_T", "sample_49_T", "sample_50_T" ], "rows": 242, "table": true, "tojson": true }, { "name": "phenotypes", "title": "", "object": "juncExprsSimulated", "file": "juncExprsSimulated.rda", "class": [ "factor" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "GSReg-package", "title": "A package for Gene Set Analysis based on the variability of gene expression in different phenotypes.", "topics": [ "GSReg-package", "GSReg" ] }, { "page": "GSReg_GeneSets_DIRAC", "title": "Performs DIRAC for gene set analysis from the paper Eddy et al (2010).", "topics": [ "GSReg.GeneSets.DIRAC" ] }, { "page": "GSReg_GeneSets_VReg.", "title": "Performs Gene Set Analysis using Expression Variation Analysis (EVA).", "topics": [ "GSReg.GeneSets.EVA" ] }, { "page": "GSReg_Kendall", "title": "Calculate Kendall-tau distance in different forms", "topics": [ "GSReg.kendall.tau.distance", "GSReg.kendall.tau.distance.restricted", "GSReg.kendall.tau.template" ] }, { "page": "GSReg_OverlapJunction", "title": "Generates junction overlap matrices required for SEVA", "topics": [ "GSReg.overlapJunction" ] }, { "page": "GSReg_SEVA", "title": "Applies Splice-EVA (SEVA) algorithm", "topics": [ "GSReg.SEVA" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "GO.db", "graph", "Homo.sapiens", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lifecycle", "memoise", "mime", "openssl", "org.Hs.eg.db", "OrganismDbi", "pkgconfig", "png", "R6", "RBGL", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Vectors", "Seqinfo", "snow", "sys", "TxDb.Hsapiens.UCSC.hg19.knownGene", "vctrs", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "GSReg.Rnw", "filename": "GSReg.pdf", "title": "Working with the GSReg package", "engine": "utils::Sweave", "headings": [ " Introduction ", " Input Data ", "Analysis of the pathways", " System Information", " Literature Cited " ], "created": "2014-07-17 23:30:16", "modified": "2018-11-16 19:30:29", "commits": 5 } ], "_score": 4.056904851336473, "_indexed": true, "_nocasepkg": "gsreg", "_universes": [ "bioc", "afsari" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-10-07T10:45:02.000Z", "distro": "resolute", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/abb47cefcdae02bbf8f55f6d5e2d06653c575e81ea06cfdf44306a1b1bf0cf62", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-10-07T10:47:08.000Z", "distro": "resolute", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/c654629a98d4614e4eefc4f2ac3d9c94cda940f87fbd357d0469a35c8dc61b26", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-10-07T10:44:50.000Z", "distro": "resolute", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/da1c25758c53e7bbd8167915e825447dafe31ca17f63f8144b5d293d0b00dabe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.1", "os": "linux", "version": "1.47.0", "date": "2026-10-07T10:46:27.000Z", "distro": "resolute", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/ec00154df6a0609adab8a0bc816337dc66aa203376f5f8ea5f9eac7764bde3aa", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-10-07T13:18:20.000Z", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/61bb2c39cea52b6277e61c9ab383fc23471a5b0c256cc0da9fef5f16cd7724b9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-10-07T13:01:19.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/0494b00fe1fe23ee22dea98d37653ebc90321bd822833c7cce49b2ad7deff54d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-10-07T13:18:14.000Z", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/deb819a32ed6f404c2623f4c1380256bfeac1779cfa9b07dcd2edabb591e814e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.1", "os": "mac", "version": "1.47.0", "date": "2026-10-07T12:58:58.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/a8a1dfc649e0b669f09a5f09167a74a5f1bb78a265bfea6b182b0473d1f55020", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-10-07T10:45:05.000Z", "arch": "emscripten", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/df7ae9acd03ed6fb1c2270c704d1557eacc5481e88ce46ee78f3f1fbaa73dd88", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-10-07T10:45:20.000Z", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/5ca78556464f6b611ba0fdb89788c01ca60751c6dc06cb804e9b927d97d81126", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-10-07T10:46:10.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/5e259da3c9a0730dc858fb0db49b2be6227e9e05b53ec95c94c1f6b8d2d9ce2d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-10-07T10:46:23.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/f6e65754da414b4dffdbeb67ed24cee740d0a11f222c2b5d4af18afedc8494ef", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-10-07T10:45:48.000Z", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/598f022e9102708beaec1bffe071cdf54389b1b37cdd5435000921caccb2373a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" }, { "r": "4.6.1", "os": "win", "version": "1.47.0", "date": "2026-10-07T10:45:50.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "https://r2.ropensci.org/f38f94fb4f5848b16a506fe8e35ca7b279f1ea38f0b91a67aa265959efd02951", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/37608430539" } ] }